To get an output by combining fields from two different files Post: 302240626

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Top Forums Shell Programming and Scripting To get an output by combining fields from two different files Post 302240626 by smriti_shridhar on Friday 26th of September 2008 06:56:23 AM

09-26-2008

Registered User

To get an output by combining fields from two different files

Hi guys,
I couldn't find solution to this problem. If anyone knows please help me out.
your guidance is highly appretiated.

I have two files -

FILE1 has the following 7 columns ( - has been added to make columns visible enough else columns are separated by single space)

155.34 - leg - 1 - 344 - TC200232 - 292 - 930
152.88 - leg - 1 - 344 -TC215306 - 2 - 743
123.94 - leg - 1 - 344 -TC210135 - 423 - 1148

FILE2
>TC200232.pep
AYNGFNNSNIIRDGVAIINSSGALKLTNRSYNVIGHAFHPNPVPIFNSSTKNVTSFSTYF
VFAIVPLEKTSGGFGFA
>TC210135.pep
GFGDFGKDSNFESQIALYGDAKVVNGGIQMSGSMGFSAGRILNKKPFKLIDGNPRKMVSF
SLHFVFSLSRENGDGFAFVMVPIGYPFDVFDGGSFGLLGNRKMKFLAVEFDTFMDEKYGD
VNDNHVGVDLSS
>TC215306.pep
PRLKQDLTLVGSVIVSDEKKSVQIPDPEREGDDLKHLVGRAIYSSPIR

I want an output like this - FILE3 - which is same as FILE2 but the line starting with '>' should also contain (region 292 to 930 of SEQ) where 292 and 930 are the corresponding columns 6 and 7 of FILE1 for the common id i.e. TC200232 (present in both the files)

>TC200232.pep (region 292 to 930 of SEQ)
AYNGFNNSNIIRDGVAIINSSGALKLTNRSYNVIGHAFHPNPVPIFNSSTKNVTSFSTYF
VFAIVPLEKTSGGFGFA
>TC210135.pep (region 423 to 1148 of SEQ)
GFGDFGKDSNFESQIALYGDAKVVNGGIQMSGSMGFSAGRILNKKPFKLIDGNPRKMVSF
SLHFVFSLSRENGDGFAFVMVPIGYPFDVFDGGSFGLLGNRKMKFLAVEFDTFMDEKYGD
VNDNHVGVDLSS
>TC215306.pep (region 2 to 743 of SEQ)
PRLKQDLTLVGSVIVSDEKKSVQIPDPEREGDDLKHLVGRAIYSSPIR

Last edited by smriti_shridhar; 09-26-2008 at 08:03 AM.. Reason: formatting

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LEARN ABOUT LINUX

comm

COMM(1) 							   User Commands							   COMM(1)

NAME

       comm - compare two sorted files line by line

SYNOPSIS

       comm [OPTION]... FILE1 FILE2

DESCRIPTION

       Compare sorted files FILE1 and FILE2 line by line.

       With  no  options,  produce three-column output.  Column one contains lines unique to FILE1, column two contains lines unique to FILE2, and
       column three contains lines common to both files.

       -1     suppress column 1 (lines unique to FILE1)

       -2     suppress column 2 (lines unique to FILE2)

       -3     suppress column 3 (lines that appear in both files)

       --check-order
	      check that the input is correctly sorted, even if all input lines are pairable

       --nocheck-order
	      do not check that the input is correctly sorted

       --output-delimiter=STR
	      separate columns with STR

       --help display this help and exit

       --version
	      output version information and exit

       Note, comparisons honor the rules specified by `LC_COLLATE'.

EXAMPLES

       comm -12 file1 file2
	      Print only lines present in both file1 and file2.

       comm -3
	      file1 file2  Print lines in file1 not in file2, and vice versa.

AUTHOR

       Written by Richard M. Stallman and David MacKenzie.

REPORTING BUGS

       Report comm bugs to bug-coreutils@gnu.org
       GNU coreutils home page: <http://www.gnu.org/software/coreutils/>
       General help using GNU software: <http://www.gnu.org/gethelp/>
       Report comm translation bugs to <http://translationproject.org/team/>

COPYRIGHT

       Copyright (C) 2010 Free Software Foundation, Inc.  License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to the extent permitted by law.

SEE ALSO

       join(1), uniq(1)

       The full documentation for comm is maintained as a Texinfo manual.  If the info and comm programs are properly installed at your site,  the
       command

	      info coreutils 'comm invocation'

       should give you access to the complete manual.

GNU coreutils 8.5						   February 2011							   COMM(1)

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